Rice Emboss Bosc2009

EMBOSS European Molecular Biology Open Software Suite Peter Rice pmr@ebi.ac.uk

A quick introduction

Open source package for sequence analysis

ANSI C source code

GPL licensed applications, LGPL libraries

200+ applications

100+ third party applications in 15 associated packages

Project started 1996 at Sanger and HGMP

Now based at EBI

Release 6.1.0 15th July 2009

Funded by UK-BBSRC and EMBL-EBI

BOSC: EMBOSS 2009 29.06.09

A near death experience

April 2004: The UK Medical Research Council decided to close the UK Human Genome Mapping Project Resource Centre (now the Rosalind Franklin Institute)

That was where all the EMBOSS developers worked

We announced the potential end of EMBOSS development to our user community

HGMP closed in July 2005

The developers moved to EBI, interim funding to April 2006.

Funding was secured in May 2006 (BBSRC)

… and again in May 2009 (BBSRC)

As far as we are aware, all our academic and industry users continued running EMBOSS … with no risk

That is a huge advantage for open source licensing

BOSC EMBOSS 2009 29.06.09

Who do we serve?

Expert software developers

Bioinformaticians

Computer scientists

Expert users

Biology research community

Industry

Scientific users

Biology research community

Industry

BOSC: EMBOSS 2009 29.06.09

EMBOSS World Wide BOSC: EMBOSS 2009 29.06.09 We have users in every continent - and a picture to prove it. This is British Antarctica. We are promised another photo from the frozen North The first EMBOSS course was in Beijing, April 1999. The wEMBOSS interface is from Canada, Argentina and Belgium

EMBOSS command line interface

EMBOSS applications run from the command line

This is not the only interface

There are over 100 interfaces and packaged systems available

All applications have a command definition file (.acd)

Defines all inputs, outputs, and other options

Read at startup

Contains all command line options with descriptions

Template for any other interface

BOSC: EMBOSS 2009 29.06.09

EMBOSS command line example

% antigenic

Input protein sequence(s): uniprot:actb1_fugru

Minimum length of antigenic region [6]:

Output report [actb1_fugru.antigenic]:

% antigenic uniprot:actb1_fugru -auto

BOSC: EMBOSS 2009 29.06.09

EMBOSS ACD File

application: antigenic [

documentation: "Finds antigenic sites in proteins"

groups: "Protein:Motifs"

]

section: input [

information: "Input section"

type: "page"

]

seqall: sequence [

parameter: "Y"

type: "PureProtein"

]

endsection: input

section: required [

information: "Required section"

type: "page"

]

BOSC: EMBOSS 2009 29.06.09 integer: minlen [ standard: "Y" minimum: "1" maximum: "50" default: "6" information: "Minimum length of antigenic region" ] endsection: required section: output [ information: "Output section" type: "page" ] report: outfile [ parameter: "Y" rformat: "motif" multiple: "Y" taglist: "int:pos=Max_score_pos" ] endsection: output

EMBOSS makes things easy

ACD files define sequence input

Sequence type for DNA/protein, possible ambiguity codes, gaps

Sequences in files

40+ formats supported - auto detection

Sequence databases

Remote servers

SRS, Entrez, MRS

User-specified URL

Locally indexed - using the original data files

Local script utilities

BOSC: EMBOSS 2009 29.06.09

EMBOSS Web Interface BOSC: EMBOSS 2009 29.06.09 http://emboss.ch.embnet.org/wEMBOSS/

EMBOSS SoapLab Service BOSC: EMBOSS 2009 29.06.09 MyGrid/EMBRACE projects: for use by Taverna Workflows

EMBOSS User Survey BOSC: EMBOSS 2009 29.06.09

EMBOSS Update

Release 6.1.0 as usual on 15th July 2009

New EMBL and UniProt formats

With full set of cross-references

FASTQ short read formats

Jemboss GUI included as standard

Further profiling for enhanced efficiency

2000+ QA tests (more needed)

Updated Phylip 3.68 … and file format variants

Services for EMBRACE/SoapLab2

DAS testing

BOSC: EMBOSS 2009 29.06.09

Example Dasty screen:

Example Ensembl screen:

EMBOSS Future plans

Three open source books: users, developers, admin

Cambridge University Press

Original text can be freely reused

New areas of interest

Metadata and ontologies (EDAM, taxonomy, GO, SO, …)

(all) public data resources

Coordinate systems (ensembl, gene/protein input/results)

Project-based working

Next-generation sequence data – used by ordinary biologists

100+ new applications

Database index updates

Scientific advisory board

Developer courses: anywhere, any time

BOSC: EMBOSS 2009 29.06.09

The Emboss Team BOSC: EMBOSS 2009 29.06.09 Peter Rice Alan Bleasby Jon Ison Mahmut Uludag Mon 12:15 Technology Track Mon 17:45 Poster U43 Wed 13:00 Birds of a Feather

Acknowledgements

EBI: Peter Rice, Alan Bleasby, Jon Ison, Martin Senger, Tom Oinn, Jaina Mistry, Rodrigo Lopez, Sharmilla Pillai, Hamish McWilliam

RFCGR/HGMP: Alan Bleasby, Jon Ison, Tim Carver, Hugh Morgan, Claude Beazley, Lisa Mullan, Damian Counsell, Gary Williams, Val Curwen, Mark Faller, Sinead O’Leary, Thon deBoer, Martin Bishop

LION: Thomas Laurent, Bijay Jassal, Bren Vaughan, Thure Etzold

Sanger Institute: Ian Longden, Richard Bruskiewich, Simon Kelley

National bioinformatics service providers in: Norway, Spain, Italy, Netherlands, Germany, Belgium, Russia, China, Canada, Australia, Argentina

Others: Catherine Letondal, Don Gilbert, Rodger Staden, Bill Pearson, Webb Miller, Marie-Laetitia Denayer, Amandine Schurmann, Gabriele Weiler, Luke McCarthy, David Mathog, David Bauer, Henrikki Almusa, Thomas Siegmund, Scott Markel, Darryl Leon, Bastien Chevreux...